Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagtgactattctacatgtattggtagcatttttctttttccgtagcacaactttattgaatcattgttcccctacctcttacacctgtttcccttctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTTGTCACTAGAACATTGGCAAACGGTCAAGGAACTAGAGAGGCTGCGAAGA

Basic information

species Glycine max
transcript GLYMA04G39990.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39990.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv13s0067g02530.t01 (Vitis vinifera), 3'ss of exon 13
gttagttagtgactattctacatgtattggtagcatttttctttttccgtagcacaactttattgaatcattg-ttcccctacctcttacacctgtttcccttctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTTGTCACTAGAACATTGGCAAACGGTCAAGGAACTAGAGAGGCTGCGAAGA
                          || ||       || ||||    |  ||   |||| ||  ||  ||| |||  ||    ||  || |   |  | ||  |  |||||||| | ||||||||||| || |||||  |||| |||||||| |||  ||||||| | ||||||||||||| ||| || ||||| ||||||||  |||| 
-------------------------gttagtcatgggattgttttgtgatttcaactctttgttccatgtttggttctactgaggct--catcgact--cttttgcttacagATTGCTGACAATGGGCCGGCTAATGTCTCTGAGTTATGGTGAAACCTCCTTGTCATTGGAACATTGGCAAATGGTGAAAGAACTGGAGAGGCTAAGAAGG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|14205839|gb|BG839517.1|BG839517
EST:     GCAGACAGGGAGCTTGAGCTCCCAAGACTTAAGCAG                         ATTGGTACCAATGGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCT
genomic: GCAGACA-GGAGCTTGAGCTCCCAAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAAT-GGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCT
EST: gi|192294723|gb|FG986572.1|FG986572
EST:     GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAG                         ATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGGGGAGACCAGCT
genomic: GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTG-AGACCAGCT
EST: gi|7235080|gb|AW570470.1|AW570470
EST:     CAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAG                         ATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
genomic: CAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
EST: gi|207820911|gb|GD791824.1|GD791824
EST:     AAGACTTAAGCAG                         ATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
genomic: AAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
EST: gi|22933040|gb|BU550179.1|BU550179
EST:     GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAG                         ATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
genomic: GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTT
EST: gi|5605823|gb|AI899921.1|AI899921
EST:     GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAG                         ATTGGTAACANTGGGCCGTCTCATGTCATTG
genomic: GTTGCAGCAAGACAAGCAGACAGGAGCTTGAGCTCCCAAGACTTAAGCAGgttagttagt ... tctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttattgaatcattgttcccctacctcttacacctgtttcccttctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTTGTCACTAGAACATTGGCAAACGGTCAAGGAACTAGAGAGGCTGCGAAGA
                          ctcttac  putative branch site (score: 3)
              ttgttcccctacctct  CT-rich tract
     attgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttagtgactattctacatgtattggtagcatttttctttttccgtagcacaactttattgaatcattgttcccctacctcttacacctgtttcccttctcccacagATTGGTAACAATGGGCCGTCTCATGTCATTGAGCTATGGTGAGACCAGCTTGTCACTAGAACATTGGCAAACGGTCAAGGAACTAGAGAGGCTGCGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA